Abstract

Synonymous codons are not used randomly. Rather, some codons are used more frequently than others. Investigating codon usage bias is essential to the understanding of viral evolution. However the factors shaping synonymous codon usage bias and nucleotide composition in animal viruses have been studied only to a limited extent. In our study, using the 19 complete CDS sequences of Spike (S) genes of porcine epidemic diarrhea virus (PEDV), we analyzed synonymous codon usage bias. The relative synonymous codon usage (RSCU) was used to estimate codon usage variation in each gene, and the results indicated that preferentially used codons were A-ended, G-ended, and U-ended codons. Effective number of codons (ENC) values varies from 48.15 to 49.52, which suggested that the codon usage bias in PEDV S genes was very slightly. Correspondence analysis (COA) was further performed to study the major trend in codon usage variation, and the plot of ENC values against GC3s (at synonymous third codon position) revealed that mutational pressure rather than translational selection was the main factor determining the codon usage bias in PEDV S genes. Moreover, correlation analysis indicated that aromaticity and hydrophobicity of S genes also influenced the codon usage variation in a minor way. Our study provides the most comprehensive analysis to date of PEDV S genes’ codon usage patterns and provides a basic understanding of the mechanisms for codon usage bias.

Key words: Porcine epidemic diarrhea virus, Spike gene, relative synonymous codon usage, effective number of codons, correspondence analysis, correlation analysis.